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NM_000262.3(NAGA):c.1209C>T (p.Ile403=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 12, 2018
Accession:
VCV000719610.3
Variation ID:
719610
Description:
single nucleotide variant
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NM_000262.3(NAGA):c.1209C>T (p.Ile403=)

Allele ID
729224
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.2
Genomic location
22: 42060306 (GRCh38) GRCh38 UCSC
22: 42456310 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.42456310G>A
NC_000022.11:g.42060306G>A
NG_009247.1:g.15537C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000022.11:42060305:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00104
The Genome Aggregation Database (gnomAD) 0.00126
Exome Aggregation Consortium (ExAC) 0.00091
The Genome Aggregation Database (gnomAD) 0.00201
Links
dbSNP: rs201582948
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Sep 12, 2018 RCV000892789.1
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001145650.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 10, 2018 RCV001145649.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NAGA - - GRCh38
GRCh37
105 157

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 12, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001036689.1
Submitted: (Mar 14, 2019)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Alpha-N-acetylgalactosaminidase deficiency type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001306340.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Alpha-N-acetylgalactosaminidase deficiency type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001306341.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Sep 10, 2018)
criteria provided, single submitter
Method: clinical testing
Alpha-N-acetylgalactosaminidase deficiency type 1
Allele origin: germline
Invitae
Accession: SCV001726373.1
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs201582948...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021